So when I'm playing KH2 it runs beautifully, until I get to a cutscene or the end of a fight where the game itself goes into a slowmotion pan or anything of the sort. The game will suddenly slow down to 70% but only in these moments, any other time during a cutscene or gameplay it's at 100% with no stutters. Just wondering why this is and if there is a fix for this issue?

What does the EE and GS say in the game window title bar during those times?
Just for a test try disabling AA and set the resolution to native
Check if during the cut scenes the title bar say GSdx HW not SW
Since you are on nvidia card,try using OpenGL from GSdx
And finally if nothing helps,try using the latest beta of pcsx2http://buildbot.orphis.net/pcsx2/